These are the Churches where you can find religious people good with children, animals, and the elderly. Kindly priests and other religious types ready to give help or good advice to any troubled heroes are to be had here, and in the more fantastical types of setting, clerics willing to give healing of both the physical and spiritual to the wounded adventurer and resurrect the occasional dead team mate. Should the heroes ever meet the Pope or local equivalent of this church, more often than not, they will find themselves standing before a Reasonable Authority Figure very ready to hear what they say.

Generally, in Speculative Fiction settings, the more likely you have an Exclusively Evil monster race that is hurt by holy powers, the more likely it is that the church will be good instead of evil. Sometimes this kind of Church may be portrayed besides one of the corrupt or evil ones for contrast and to help emphasize the pure goodness of the religion.

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The Belkan Saint Church in Magical Girl Lyrical Nanoha, who in addition to building schools and hospitals, also provides assistance to the Time-Space Administration Bureau whenever they can. In the third season, the Bureau itself (for whom all of the protagonists work) has been revealed to have a darker side, so the Saint Church remains as the only incorruptible authority in the setting.

Mahou Sensei Negima has a church-related arc, wherein the clergy are supposed to be of the "kindly old man" variety, even though we never do meet them. Made ironic (possibly subverted?) by the fact that the local nuns are, in fact, mages.

The Royal Order of Protestant Knights, and Iscariot Division XIII from Hellsing, while appallingly brutal in battle against Millennium (and occasionally each other), act for the good of the Crown, the Church, the Vatican, and the people under their care. There are zealots who go too far, such as Maxwell, but most (like Anderson and Integra) have high moral standards, even if they are unapologetic fanatics for their beliefs. To be fair, their enemies are Nazi vampires. This is exemplified by Anderson's first appearance in the first anime: the Trenchcoat Brigade scarred giant of a man gives a stewardess a start but then produces a genuinely warm smile and blesses her (in the best Norio Wakamoto voice)--for no other reason than to dispel her fears.

The church, and holy men in general are generally portrayed positively in the Hellboy comics. Most priests are pretty nice guys and their blessings are genuinely effective against minor demons, though big ones like Helldad can shrug them off. Even vicious ones like the Inquisitors from The Island and the Witchfinder General were usually the lesser of two evils. What makes this rather odd is that the Mignolaverse's cosmology, aside from having some sort of God and a Hell full of demons bears little resemblance to any major religion.

For the most part, the Catholic Church in Warrior Nun Areala is portrayed very positively, as being an organization working directly under the authority of Heaven, empowered to hunt down and battle the forces of Hell, and optionally more mundane villainy such as Nazi masterminds. The order of Warrior Nuns is armed with weapons that, while lethal to demons and the undead, do not harm humans.

In Marvels What if... story where Wolverine became the Horseman of War future is an wannabe-utopia where humanity has united under the threat of War (as in Wolverine, not war). There are retreats, held by monks, for people who wish to practice peace more than the other people. The monks are the ultimate keepers of peace, teaching the way on non-violence in a world without war. One of the monks is Brother Xavier, who really is Wolverine, who has learned how to keep his anger in control.

Almost all of the religious organizations in The Dresden Files. Most specifically Father Forthill's church. But there's also the Buddhist monastery that Mouse the Lion Dog puppy came from.

The churches run free hospitals in Jennifer Government, where everything down to the ambulance service is privatised. Volunteers for the hospitals take the hospitals name as a auxiliary surname.

The Christian Church in Quo Vadis? is unambiguously good. Its members live simple, happy lives, standing above the depraved environment surrounding them in Ancient Rome.

In the backstory to H.P. Lovecraft's The Haunter of the Dark, the evil Nyarlathotep-worshiping cult are routed by a Catholic/Baptist alliance between Father O'Malley and the Reverend Drowne. At the climax of the story, a group of Italian Catholics attempt to contain the avatar of Nyarlathotep within its prison using candles, but, sadly, it slips through.

From the Honor Harrington series, most religions are implied to be this, including Second Reformation Catholic (Queen Elizabeth III), Third Stellar (Honor herself) and the Church of Humanity Unchained (Grayson edition), which, although highly conservative and somewhat sexist, is largely good - personified in leader Reverend Hanks. Obviously, the Masadan variant - well, not so much.

The Universal Brotherhood in E.C. Tubb's "Dumarest" books. The "monks" are pacifistic, doing good among the downtrodden, oppose the machinations of the Cyclan, and frequently assist Dumarest against them.

The Way of the Prophets in Star Trek: Deep Space Nine. Granted, for most of the series its leader is Sinister Minister Kai Winn, but it's made clear that she doesn't really have that much influence on what the church itself believes, and her subordinates continue to be Good Shepherds.

The Church of Pelor... and pretty much every church of good aligned deities in Dungeons & Dragons that are on the ball.

Other major examples in the Third Edition standard cosmology are Hieronious, Kord, Moradin, Corellon Larethiean, Garl Glittergold, Yondala, and Bahumat.

In the Forgotten Realms setting, Ilmater tends to be this especially, but then, he is Crystal Dragon Jesus more than most. Also the divinely-granted spells of the worshipers of Sune, Goddess of Beauty and Love, are the closest thing to weaponized love in the setting.

A good Eberron example is the ancestor-worship of the Elves of Aerenal, which is Neutral Good and splits its time equally between giving advice to the still-living Elves and beating seven shades of undead crap out of the Blood of Vol.

Also Temple of Shallya, goddess of healing and mercy. And non-violence, what is quite hard a commitment in such a violent world as Warhammer. Church of Sigmar is the good guys, but it's more an example of Lawful Good Church Militant.

The Brotherhood from Mutant Chronicles. They run charitable hospitals, schools and soup kitchens, maintain the only universally recognized bank and currency, and mediate in corporate disputes. Granted, they also torture suspected devil-worshipers and assassinate dissidents, but in a time when the legions of Hell have already conquered 2/3 of the Solar System once, were only driven back because the Brotherhood intervened, and are looking to infiltrate human society and make a repeat performance this may not be a bad thing...

The Church of Avacyn on the plane of Innistrad is the only shining beacon of hope for humanity in a plane full of many horrors, most of them undead in one way or another. The church employs various Catholic-esque imagery, such as the Mark of Avacyn, a vaguely cross-like symbol used in many of the same contexts, and naming its prominent members as "Saints" (during life rather than posthumously). Unfortunately, its patron angel Avacyn is AWOL.

Danette's parents were part of one of these in Soul Nomad and The World Eaters. One was a priest, the other a mage. Revya's group also protects one of these from Thurists.

The Church of the Holy Light in Warcraft 'verse. Their offshoot, the Scarlet Crusade, is lessso. Disgruntled members of the Scarlet Crusade also have their own reformist organization, the Argent Dawn, which is an equal-opportunity employer and even has high-ranking undead members.

The Church of the Holy Maiden in La Pucelle; although the game actually questions the notion of faith in gods at some points (and even their goddess, Poitreene, herself claims not to be perfect at one point ) the Church is still largely a force for good that cares for the people. On the other hand their rivals, The Church of the Holy Mother, turns out to be a Religion of Evil in disguise but has more worshipers.

The Air Nomads in Avatar: The Last Airbender are heavily implied to have been a Buddhist-inspired variation of this, mostly according to the backstory and a lot of Word of God. They used all the money they made to support others, they fought only in self-defense, and the last surviving Air Nomad, the eponymous Last Airbender, makes reference to various Air Nomad wisdom from time to time. It's notable that as a whole, they were so spiritual that their entire culture could Airbend, while in the other Nations only a certain percentage can, though this may be related to their small population.

This is so much a part of airbender culture that in one late episode, when Aang is conferring with his past incarnations to try and find a relatively peaceable solution to the problem of Fire Lord Ozai, he almost has a Heroic BSOD when even previous Air Nomad Avatars counsel killing Ozai as the best solution.